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In Front Misson 3, you make a choice early in the game that determines which of two plots your game will follow. In one path, Emma joins your party. In the other path, Alisa joins your party. Also, since the paths have different plots, you fight in different battles.

What other differences exist between the 2 plot paths?

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What's different besides a different story and a different set of enemies in different locations? Not much.

Of course, just with those few differences, you've already got an almost entirely different game. IIRC, one of the main side-effects of that choice is that you're choosing between a "missile-based" ally and a "close combat" ally.

I think the most important difference is the set of enemies you're up against, because that determines what skills your pilots are going to pick up. One story leads very quickly to the powerful "Pilot DMG" skills which then allows you to capture complete wanzers by taking out the pilot without totally destroying wanzer parts.

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Different stories, with different locations equals "not much?" LOL. Here's a few more specifics:
>>> The number of battles it takes to finish the game differ; Emma's has more.
>>> Certain characters appear as party members in one story and opponents in the other - Liu, Marcus, Yun, Lan, Pham. You fight Jose in both, but can only recruit him afterwards in Emma's (I personally recommend you decline him, so that you can instead pick up Li, and his better wanzer, later in the game). Some characters don't appear at all in the other storyline (Miho only in Alisa's, unless you count the Ten-Mou wallpaper, and Li only in Emma's),
>>> The Meledyne wanzer is only available in Alisa's story; the Drake (and its "Chaff" defensive skill) and Qibing 0 wanzers only in Emma's (and you have to capture a Qibing to get it). At least you can carry skills from one storyline into the other as a playthrough.
>>> Kyokei wanzers (and parts) are harder but not impossible to find in Emma's story (must be unlocked, you don't get Miho's if she isn't present). Worth having, as Kyokei legs are light enough to mount on a missile unit, which doubles its mobility!
>>> Emma's story has many more internal branches and subdivisions. The end result of the Cadenza battle, and how you tackle the battle at the dam affect other things.

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